So I went to "data management -> programs to rebuild" the game database and it fixed my problem and I formatted the emunand and made the initial setup for the second time. Then I changed my theme for precaution then I realised my nands had become linked because my menuhax settings were removed in my sysnand and I had to install it again.

EDIT: Sorry, didn't read everything >.<, try using tinyformat again until they are confirmed unlinked, if that doesn't work out you can also try downgrading and ignore them being linked, I did that in the past and it worked, but I would rather try to unlink them.